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I very often feel the need of posting a comment to simply say thanks for some idea in a comment, like a nice reference or a pedagogic suggestion, or simply to remark that the answer I accepted was the best one but anyway the other answer was helpful too.

That comments are not physics, strictly speaking they are sort of noise. Provided that one tries to restrict them to a discreet minimum, are they bad and should be avoided? (Note that I already know that comments can be upvoted, though anonymously)

Tha... sorry. You see? It's difficult...

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    $\begingroup$ This is a good question, I've asked it myself several times already but I've almost always strictly followed the 'rules', not posting such comments. However, as Dilaton and Manishearth point out: I think those comments (as well as light-hearted/witty comments) make the site more human and welcoming (warmer). And indeed they give clues about what the differences are between a good answer and a brilliant one. These comments should never dominate, but they shouldn't be forbidden either. I think Gugg and AlanSE are on the right track as well. Upvotes all around! $\endgroup$ – Wouter May 12 '13 at 1:29
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Some people dont like such comments and say it is noise because Physics SE is not a social network, etc. etc. indeed; but I personally think they make the site more friendly, human, nice and welcoming to everybody.

When looking around at Meta Stack Overflow I note that some people consider being friendly to each other by posting some additional nonessential nice comments (and even reading them) a waste of time, nuisance, etc. If I get it right this is related to the awful term "Big City Problem", by which these people justify having not the time to be nice, helpful, and patient to each other by reasoning that the site is no longer a small village and related arguments.

I am happy that this (in my eyes unfriendly) attitude and way of thinking has not taken over here up to now, and I hope it never will.

So in my opinion, comments saying thanks for helpful things and more generally being friendly to each other by a few nonessential additional comments should not be restricted or even forbidden. Too long (off topic) discussions can go to chat as usual of course.

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    $\begingroup$ Agreed. Thanks for this answer. $\endgroup$ – SMeznaric May 23 '13 at 12:41
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The purpose of comments is to induce improvement into the answer. If a comment has no potential to do , it's deletable.

So try to avoid posting thank-yous willy nilly.

However, I personally encourage leaving nice comments on an answer you find particularly exceptional (unless there already are a bunch of such comments on said answer). I've received a couple of these on answers that I thought of as ordinary. Besides givng me a warm and fuzzy feeling, they have given me insights on how to write better answers.

So restricting them to a discreet minimum seems OK to me :)

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    $\begingroup$ +1 Nice answer! Indiscreetly: This is really useful, as I had to answer this question myself several times, knowing that I didn't know the community's take on this. @Dilaton's answer (the currently only other one) is also nice, he also gets a +1. :) $\endgroup$ – Řídící May 11 '13 at 20:28
  • $\begingroup$ @Gugg, in fact, now it is difficult for me to decide which answer is best. $\endgroup$ – Mephisto May 11 '13 at 20:35
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    $\begingroup$ @Mephisto Another issue is: Should you "upvote" my first comment? :) Perhaps that's a criterion: Do you think the "thank you" comment is upvoteable? If so, post it. If not, don't. $\endgroup$ – Řídící May 11 '13 at 20:40
  • $\begingroup$ Ahh... I should've posted my question here instead of chat. h-bar didn't help me..! ;-) $\endgroup$ – Waffle's Crazy Peanut May 12 '13 at 15:59
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The social aspect is always there, and a polite collaborative environment will make people stick around.

This just means that you need to package your comments with physics. If it's a fantastic answer then perhaps say "this is a great answer, I had not even considered applying method X to the problem in the Y reference frame when I asked the question."

Additionally, I see the value in wrapping up a discussion. If someone fixes the issue you had, it's good to leave a message explaining exactly how it wrapped it up and thank the person. Think of comments as messages for whoever will be doing housekeeping. You can help by clearly pointing them to what is important and not important. It may also be helpful to say why you selected it as the answer or upvoted. For instance "I was really looking for Z method here, and this answer is the only one that provides it to the full extent".

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Trying it out on @Manishearth's answer, I came to the following rule.1

Post a "thank you"-like comment if it is "upvoteable", that is, if you consider it a comment that you might "upvote" yourself if it was posted by somebody else.

Example: You might "upvote" (because you felt the same way), and therefore may post:

+1 This is absolutely f***ing brilliant! Jeez, I never thought about it this way! You rule!

Whereas you probably won't "upvote" (and therefore probably shouldn't post)

+1 Thanks, that solved my problem.

1 This being meta, the community can upvote or downvote on this answer, depending on whether they like this rule or not.

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    $\begingroup$ Hey, this is absolutely f***ing brilliant! Jeez... well, I will consider this answer. Th... er... Thanks! (WTH!) $\endgroup$ – Mephisto May 11 '13 at 20:57

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